Rookery Bay was contracted to work with Natural Resources staff in capturing and identifying species living in Naples Bay and Moorings Bay. Seine nets and otter trawls are used to capture species of fish and invertebrates inhabiting shallow (seine) and deeper (trawl) areas along the north-south gradient of Naples Bay. The study goals are to create an updated species list, compare sample sites within Naples Bay, and compare Naples Bay to other estuarine systems in southwest Florida.

Data collection began in April 2009, with bi-monthly sampling beginning in November 2009. Four trawl stations were chosen throughout the length of Naples Bay. Quarterly sampling occurs in Moorings Bay. Organisms caught in the net are measured and counted.